Adsorption behavior of cytosine and guanine nucleobases on graphyne nanosheets: A DFT study

Interactions between DNA and the acridine intercalator: A computational study

Cancer is a global public health problem characterized by deviations in the mechanisms that control cell proliferation, resulting in mutations and variations in the structure of DNA. The mechanisms of action of chemotherapeutic drugs are related to their interactions and binding with DNA; consequently, the development of antineoplastic agents that target DNA has extensively focused on use of acridine, a heterocyclic molecule that binds to deoxyribonucleic acid via intercalation, a process that modifies DNA and makes replication impossible. In this context, this study aimed to computationally investigate how acridine intercalators interact with DNA by evaluating the mechanism of interactions, binding, and interaction energies using quantum mechanics calculations. Molecular electrostatic potential (MEP) analysis revealed that acridine has well- distributed negative charges in the center of the molecule, indicative of a dominant electron-rich region. Acridine exhibits well-defined π orbitals (HOMO and LUMO) on the aromatic rings, suggesting that charge transfer occurs within the molecule and may be responsible for the pharmacological activity of the compound. Structural analysis revealed that acridine interacts with DNA mainly through hydrogen bonds between HAcridine… ODNA with bond lengths ranging from 2.370 Å to 3.472 Å. The Binding energy (ΔEBind) showed that acridine interacts with DNA effectively for all complexes and the electronic energy results (E+ZPE) for complexes revealed that the complexes are more stable when the DNA-centered acridine molecule. The Laplacian-analysis topological QTAIM parameter (∇2ρ(r)) and total energy (H(r)) categorized the interactions as being non-covalent in nature. The RGD peak distribution in the NCI analysis reveals the presence of van der Waals interactions, predominantly between the intercalator and DNA. Accordingly, we confirm that acridine/DNA interactions are relevant for understanding how the intercalator acts within nucleic acids.

First principles studies on the adsorption of rare base-pairs on the surface of B/N atom doped γ-graphyne

Rare base-pairs consists of guanine (G) paired with rare bases, such as 5-methylcytosine (5-meCyt), 5-hydroxymethylcytosine (5-hmCyt), 5-carboxylcytosine (5-caCyt), and 5-formylcytosine (5-fCyt), have become the focus of epigenetic research because they can be used as markers to detect some chronic diseases and cancers. However, the correlation detection of these rare base-pairs is limited, which in turn limits the development of diagnostic tests and devices. Herein, the interaction of rare base-pairs adsorbed on pure and B/N-doped γ-graphyne (γ-GY) nanosheets was explored using the density functional theory. The calculated adsorption energy showed that the system of rare base-pairs on B-doped γ-GY is more stable than that on pure γ-GY or N-doped γ-GY. Translocation time values indicate that rare base-pairs can be successfully distinguished as the difference in their translocation times is very large for pure and B/N-doped γ-GY nanosheets. Meanwhile, sensing response values illustrated that pure and B-doped γ-GY are the best for G-5-hmCyt adsorption, while the N-doped γ-GY is the best for G-Cyt adsorption. The findings indicate that translocation times and sensing response can be used as detection indexes for pure and B/N doped γ-GY, which will provide a new way for experimental scientists to develop the biosensor components.

Graphdiyne applications in sensors: A bibliometric analysis and literature review

Graphdiyne is a two-dimensional carbon nanomaterial synthesized artificially in 2010. Its outstanding performance is considered to have great potential in different fields. This article summarizes the work of graphdiyne in the sensing field by literature summary and bibliometrics analysis. The development of graphdiyne in the field of sensing has gone through a process from theoretical calculation to experimental verification. Especially in the last three years, there has been very rapid development. The theoretical calculations suggest that graphdiyne is an excellent gas sensing material, but there is little experimental evidence in this direction. On the contrary, graphdiyne has been widely reported in the field of electrochemical sensing. At the same time, graphdiyne can also be used as a molecular switch for DNA sequencing. Fluorescent sensors based on graphdiyne have also been reported. In general, the potential of graphdiyne in sensing still needs to be explored. Current research results do not show that graphdiyne has irreplaceable advantages in sensing. The bibliometric analysis used in this review also provides cooperative network analysis and co-citation analysis on this topic. This provides a reference for the audience wishing to undertake research on the topic. In addition, according to the analysis, we also listed the direction that which this field deserves attention in the future.

Controlled supramolecular interaction to enhance the bioavailability of hesperetin to targeted cancer cells through graphyne: a comprehensive in silico study

In the current study, the drug carrier efficiency of graphyne (GRP) for the transfer of the hesperetin (HPT) drug is evaluated for the first time. The GRP efficacy as a carrier is investigated using the density functional theory (DFT) technique to calculate various physiochemical characteristics such as dipole moment, bandgap, and chemical reactivity-descriptors for HPT, GRP and HPT@GRP complex. The non-covalent-interaction (NCI) plot indicated that GRP and HPT have weak interaction force, which is fundamental for the drug's noticeable offloading from the GRP carrier at its target location. According to frontier molecular orbital analysis, the highest occupied molecular orbital (HOMO) of HPT distributes the charge to the GRP, the lowest unoccupied molecular orbital (LUMO) during excitation. Charge transfer is further supported by charge-decomposition-analysis, which interprets the extensive overlap between HPT and GRP orbitals. In the case of the gas phase, the λ_max of the HPT@GRP-complex is redshifted by 9 nm from GRP. In the solvent phase, the λ_max value is also redshifted. These theoretically calculated spectra also match experimentally observed spectra rather well. The PET (photoinduced electron-transfer) method and electron–hole theory were used for the graphical explication of distinct excited states. The photoinduced electron transfer (PET) mechanism interprets fluorescence dimming because of interaction. Furthermore, GRP with cationic (+1) and anionic (−1) charge states (GRP^+1/−1) showed minor structural disfigurement and formed stable HPT complexes. In the current study, HRP is loading and unloading on GRP very effectively, that can potentially be used in the oncology field. Due to this theoretical study, researchers will be interested in looking at other 2D nanomaterials for drug delivery applications.

In the current study, the drug carrier efficiency of graphyne (GRP) for the transfer of the hesperetin (HPT) drug is evaluated for the first time.

Adsorption studies of nucleobases on ε-arsenene nanosheet based on first-principles research

The electronic attributes and energetics of ε-arsenene nanosheet (ε-As) are explored with regard to the density functional theory basis. Initially, based on formation energy (-3.715 eV/atom), we ensured the structural firmness of ε-As. The ε-As is used as a base substrate to adsorb nucleobases viz., adenine (A), guanine (G), thymine (T), cytosine (C) & uracil (U). The surface adsorption of nucleobases on ε-As is analysed based on band structure, the density of states, adsorption energy, energy gap variation & charge transfer. Besides, we observed the exothermic nature of binding energy (ranging from -0.453 eV to -0.819 eV) upon nucleobase adsorption on ε-As. Also, the energy gap variation & charge transfer takes place owing to adsorption of nucleobases on the ε-As sheet. The present report reveals the adsorption of nucleobases on ε-arsenene nanosheet.

The recent advancement of low-dimensional nanostructured materials for drug delivery and drug sensing application: A brief review

In this review article, we have presented a detailed analysis of the recent advancement of quantum mechanical calculations in the applications of the low-dimensional nanomaterials (LDNs) into biomedical fields like biosensors and drug delivery systems development. Biosensors play an essential role for many communities, e.g. law enforcing agencies to sense illicit drugs, medical communities to remove overdosed medications from the human and animal body etc. Besides, drug delivery systems are theoretically being proposed for many years and experimentally found to deliver the drug to the targeted sites by reducing the harmful side effects significantly. In current COVID-19 pandemic, biosensors can play significant roles, e.g. to remove experimental drugs during the human trials if they show any unwanted adverse effect etc. where the drug delivery systems can be potentially applied to reduce the side effects. But before proceeding to these noble and expensive translational research works, advanced theoretical calculations can provide the possible outcomes with considerable accuracy. Hence in this review article, we have analyzed how theoretical calculations can be used to investigate LDNs as potential biosensor devices or drug delivery systems. We have also made a very brief discussion on the properties of biosensors or drug delivery systems which should be investigated for the biomedical applications and how to calculate them theoretically. Finally, we have made a detailed analysis of a large number of recently published research works where theoretical calculations were used to propose different LDNs for bio-sensing and drug delivery applications.

The damage of the Watson-Crick base pairs by nickel nanoparticles: A first-principles molecular dynamics study

The nickel nanoparticles are harmful atmospheric pollutants, and the damage caused by them in humans has become a topic of great relevance. In this study we investigate the interaction of the Ni2 and Ni3 clusters with the AT and GC Watson-Crick base pairs in an aqueous medium. Molecular dynamics in combination with density functional theory are employed. A novel method is implemented to create realistic thermodynamic conditions (NVT) in the simulations. The energies, the charges of the interacting compounds, the temperature changes, and the geometric rearrangements are reported. The results show the formation of stable organometallic compounds of the nickel nanoparticles with the DNA nucleic acid bases. In this respect, the biological processes where the DNA is implicated may be altered by the formation of such super-structures.

Interaction studies of kidney biomarker volatiles on black phosphorene nanoring: A first-principles investigation

We report the electronic properties of black phosphorene nanoring (BPN) and adsorption behavior of chronic kidney disease biomarker vapors on BPN. The designed BPN is stable, which is ensured by the formation energy with a value of -3.857eV/atom. The band gap of BPN is recorded as 0.716eV showing the semiconductor property. The prominent kidney disease biomarker vapors, namely isoprene, pentanal, hexanal, heptanal are allowed to interact on BPN and studied based on adsorption property on BPN. Based on charge transfer, energy band gap variation and adsorption energy, we studied the adsorption behavior of BPN towards kidney disease biomarkers. Our findings show that BPN can be used to detect the presence of kidney biomarkers.